New space warping method for the simulation of large-scale macromolecular conformational changes

A space warping method, facilitating the modeling of large-scale conformational changes in mesoscopic systems, is presented. The method uses a set of "global (or collective) coordinates" that capture overall behavior, in conjunction with the set of atomic coordinates. Application of the space warping method to energy minimization is discussed. Several simulations where the method is used to determine the energy minimizing structures of simple central force systems are analyzed. Comparing the results and behavior of the space warping method to simulations involving atomic coordinates only, it is found that the space warping method scales better with system size and also finds lower minima when the potential energy surface has multiple minima. It is shown that the transformation of [Ala16]+ in vacuo from linear to globular is captured efficiently using the space warping method.     

Generation dependent mesophase behavior in extended amphiphilic dendrons in the shape of macromolecular dumbbells

Small angle X-ray scattering studies of 2nd and 3rd generation based extended amphiphilic dendrons in the shape of macromolecular dumbbells with identical hydrophilic volume fractions suggest 2-D hexagonal columnar and Pm3n micellar cubic mesophases, respectively, elucidating the role of shape induced interface curvature in mesophase formation.     

Light to work transduction and shape memory in glassy,photoresponsive macromolecular systems: Trends and opportunities

Light can wirelessly direct functional responses in photoresponsive polymeric materials and composites. The intensity, phase, and polarization of light can be spatially modulated into complex patterns with holography (intensity or polarization) or masking (intensity or phase). Deriving from these foundational properties of light, photoresponsive macromolecular systems exhibit exceeding potential to yield rapid and highly engineered macroscopic as well as spatially selectable mechanically adaptive responses useful as soft actuators or topographical surfaces in aerospace, automotive, and biomedical applications. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Molecular weights of backbones in graft copolymers

Copolymerization of a monomer X with an existing polymer yields a copolymer contaminated by poly-X homopolymer and ungrafted polymer. Measurements on the pure copolymer can yield only the molecular weights of the cumulative backbone portion and of the cumulative graft portion. However, if the grafts can be isolated, then the molecular weights of their individual chains may be determined also. Since it is not isolatable, the backbone is not amenable to similar treatment. Equations are derived for the molecular weights (of any average) of individual backbone chains; they are expressed in terms of the following experimentally accessible quantities: (i) molecular weight of original polymer; (ii) molecular weight of ungrafted portion: and (iii) fraction by weight of the original polymer which remains ungrafted. The procedure is thus the analogue, applied to the backbone, of chemical isolation applied to the grafts. The treatment has been examined for copolymers prepared by grafting acrylic acid to nylon-6 by mutual irradiation.     

Polymorphy in the stereostructure of periodic polymer backbones

We theoretically investigated the polymorphy of the stereostructures of a periodic polymer. Using the polymer's internal conformation parameters of bond lengths, bond angles, and internal rotation angles, we extended the mathematical treatment for designing polymer backbones. We considered those periodic polymers whose unit cell consists of one (m = 1), two (m = 2), or three (m = 3) kinds of atoms. Moreover, for these three types of polymers, we supposed two catenation types for the skeleton atoms; one is a “homorotatory” sequence and the other is a “heterorotatory” one. To specify the backbone's stereostructure, we introduced several conformation parameters such as the helical pitch number n, the translation distance d, and the inclination angle of the skeleton plane Θ. By combining these parameters, we can systematically understand the variety and the possible polymorphy in the stereostructure of a periodic polymer backbone. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2829–2849, 2003     

A light-harvesting array composed of porphyrins and rigid backbones

A light-harvesting array containing rigid backbones, peripherally positioned Zn-porphyrin terminals, and a free-base (Fb) porphyrin core was prepared by a convergent method where the Sonogashira coupling reaction was used in the key steps. Effective intramolecular singlet-energy transfer from the peripheral Zn-porphyrin units to the Fb porphyrin core was observed. The efficiency of the energy transfer was compared with those of reference compounds.     

Metalloporphyrins in macromolecular chemistry

The review presents an analysis of the data on the synthesis of metalloporphyrin-based polymers of different structure. Manufacturing coordination polymers via extra coordination of small molecules and fragments of high-molecular-weight compounds by porphyrin metal complexes are discussed. The main approaches to the development of functional materials based on these polymers are summarized.     

Coordination polymers with macrocyclic cages and pockets within their backbones

The reaction between the flexible ligand (1,4-bis(pyridine-2-yl-methanethio)benzene) and Ag+ produces two novel coordination polymers with macrocyclic cages or pockets contained within their backbones, depending upon the ratio of starting materials.     

Peptide amphiphile nanofibers with conjugated polydiacetylene backbones in their core

The coupling of electronic and biological functionality through self-assembly is an interesting target in supramolecular chemistry. We report here on a set of diacetylene-derivatized peptide amphiphiles (PAs) that react to form conjugated polydiacetylene backbones following self-assembly into cylindrical nanofibers. The polymerization reaction yields highly conjugated backbones when the peptidic segment of the PAs has a linear, as opposed to a branched, architecture. Given the topotactic nature of the polymerization, these results suggest that a high degree of internal order exists in the supramolecular nanofibers formed by the linear PA. On the basis of microscopy, the formation of a polydiacetylene backbone to covalently connect the beta-sheets that help form the fibers does not disrupt the fiber shape. Interestingly, we observe the appearance of a polydiacetylene (PDA) circular dichroism band at 547 nm in linear PA nanofibers suggesting the conjugated backbone in the core of the nanostructures is twisted. We believe this CD signal is due to chiral induction by the beta-sheets, which are normally twisted in helical fashion. Heating and cooling shows simultaneous changes in beta-sheet and conjugated backbone structure, indicating they are both correlated. At the same time, poor polymerization in nanofibers formed by branched PAs indicates that less internal order exists in these nanostructures and, as expected, then a circular dichroism signal is not observed for the conjugated backbone. The general variety of materials investigated here has the obvious potential to couple electronic properties and in vitro bioactivity. Furthermore, the polymerization of monomers in peptide amphiphile assemblies by a rigid conjugated backbone also leads to mechanical robustness and insolubility, two properties that may be important for the patterning of these materials at the cellular scale.     

Adamantanes, nortricyclenes, and dendrimers with extended silicon backbones

By reaction of the hexabromoheptasilane MeSi(SiMe(2)SiMeBr(2))(3) (1 a) with H(2)O, H(2)S, NH(3), and H(2)NMe the heptasilaadamantanes MeSi(SiMe(2)SiMeO)(3) (4), MeSi(SiMe(2)SiMeS)(3) (5), MeSi(SiMe(2)SiMeNH)(3) (6 a), and MeSi(SiMe(2)SiMeNMe)(3) (6 b), respectively, were prepared in good to moderate yields. Molecular structures of 4, 5, 6 a, and 6 b were determined by X-ray crystallography. The symmetry of the cages is approximately C(3v), and the geometry around the nitrogen atoms is essentially planar. Ab initio SCF/HF calculations with the 6-31G* basis set confirm these results. Reduction of MeSi(SiMe(2)SitBuBr(2))(3) (1 b) with lithium naphthalenide afforded the heptasilanortricyclene MeSi(SiMe(2)SitBu)(3) (7). The (29)Si NMR spectrum of 7 consists of three signals with chemical shifts that agree closely with values predicted by ab initio calculations. (29)Si INADEQUATE spectra also strongly support the nortricyclene structure. Ab initio SCF/HF calculations were performed for the parent molecule Si(7)H(10), and the ring strain of the cage was estimated as 168.8 kJ mol(-1) by using the homodesmic reaction Si(7)H(10) + 3 Si(2)H(6)-->Si(13)H(28). Compound 1 a also served as the starting material for the preparation of first-generation dendrimer 2 a by reaction with six equivalents of Ph(2)MeSiLi. Subsequent protodearylation with HBr and reaction with (Me(2)PhSi)(2)SiMeK afforded second-generation dendrimer 3. All dendrimers were characterized by multinuclear NMR spectroscopy.     

Structure and reactivity of phosphorus-selenium heterocycles with peri-substituted naphthalene backbones

Reaction of naphthalene-1.8-bis(dichlorophosphine) with sodium selenide and selenium gives naphthalene-1,8-diyl)-1,3,2,4-diselenoxodiphosphetane 2,4-diselenide (27), a molecule with its four-membered PSePSe ring spanned by a naphthalene-1,8-diyl backbone. 27 was fully characterised, including by X-ray diffraction. Unusually, the reaction yielded not only 27, but also a polymeric or oligomeric material that was selenium deficient, containing significant amount of species with phosphorus atoms not fully oxidised to P(V). Reactions of the selenium deficient material with simple alcohols afforded two 1,2-diphosphaacenaphthenes, which were structurally characterised.     

Biomaterials and biofunctionality in layered macromolecular assemblies

Recent research in the field of LbL assembly is summarized and categorized as fabrication, sensing, drug release/delivery, and cell technology. Special emphasis is given to topics such as cell-membrane-mimic assembly, fabrication of free-standing biomolecular structures including protein microtubes, detection of DNA adducts and reactive metabolites, DNA hybridization analysis, sensing of toxic and bio-active chemicals, entrapment of proteins and DNA, biocomponent carriers with barcode encoding, release and delivery of DNA plasmids, multiagent delivery, smart defense capsules and oxidation-resistant films, vector introduction to cells, patterned cell culturing and microfluidic microreactors, stem cell differentiation, cellular uptake and degradation, and control of cellular apoptosis.     

Oligoarenes as molecular backbones of catalysts: synthesis and applications

This feature article highlights our recent work on oligoarene-type catalysts. We developed a synthetic method for multifunctionalized oligoarenes using a repetitive two-step strategy. The method was then applied to the preparation of oligoarene-type phosphines, which were used for palladium-catalyzed cross-coupling of halobenzenes with Grignard reagents.     

Coplanarity in the backbones of ladder-type oligo(p-phenylene) homologues and derivatives

p-Tolyl-substituted ladder-type oligo(p-phenylene)s containing three, four, and five phenylene rings were readily synthesized. The uniform aryl substitution of these systems allowed us to determine the coplanarity of the pi-conjugated backbones crystallographically. The intramolecular annulations eliminate almost all of the conformational disorder and enhance the degree of pi-conjugation of the backbones, resulting in significant red shifts in the absorption and emission maxima and lower oxidation potentials in the higher homologues. [structure: see text]     

Thermogravitational effect in macromolecular solutions

We have investigated in a thermogravitational apparatus the behavior of solutions containing macromolecular solutes and of suspensions of ultramicroscopic particles such as viruses and ribosomes. We have obtained very high separation ratios with all the solutes studied, the value of the separation being characteristic of each solution. The reproducibility of the results is good, and the dependence on the geometrical and physical parameters involved fits the predictions of the phenomenological theory. Our results prove that fractionation of very high molecular weight particles is feasible by this method, and also that the characterization of the macromolecular species and the determination of the mass and shape of the particles of the solute seem to be within the possibilities of the thermogravitational method when this is applied to very high molecular weight materials.     

Hyperelectronic polarization in macromolecular solids

Hyperelectronic polarization may be viewed as the electrical polarization in external fields due to the pliant interaction with the charge pairs of excitons, in which the charges are molecularly separated and range over molecularly limited domains. It is particularly pronounced in molecular solids composed of long polymeric molecules having extensive regions of electronic orbital delocalization. Hyperelectronic polarization is regarded as the principal contributor to the high polarizabilities of the following five macromolecular solids: four polyacene quinone radical polymers formed by condensation of aromatic hydrocarbon derivatives with aromatic acids and poly(Cu(II)-N,N′- dimethyl rebeanate). The first four polymers at 100 hz had dielectric constants of 1800–2400, decreasing to about 58–100 at 100,000 hz, with relaxation times of 10^?3 to 10^?4 sec. A sixth polymer, a Schiff-base condensate of 1,4-napthaquinone and p-toluene diisocyanate, however, showed little hyperelectronic polarization, displaying a dielectric constant of 10, constant over 100–100,000 hz. By simple arguments it is shown that the relaxation times and the frequency response of conduction are consonant with the proposed model of charges roaming over long molecular domains (up to 4000 A.) but restricted by molecular boundaries.     

Recent advances in macromolecular prodrugs

Macromolecular prodrugs (MP) are high molar mass conjugates, typically carrying several copies of a drug or a drug combination, designed to optimize delivery of the drug, that is — its pharmacokinetics. From its advent several decades ago, design of MP has undergone significant development and established solid guidelines for engineering successful MP in terms of the choice of the polymer carrier, its molar mass, and the choice of the linkage between the drug and the polymer. This review provides a brief account of the state-of-the-art in the development of MP and details the advantages of these tools of drug delivery. We also identify the challenges that need to be further addressed and offer a view on what is currently being done towards these goals. Specifically, we focus on i) the design of high molar mass, main-chain degradable polymers as drug carriers; ii) drug delivery using endogenous macromolecules such as albumin; iii) the choice of biodegradable linkages for drug delivery, and iv) the emerging interest in delivery of short-lived gasotransmitters. With this analysis and presentation, we aim to spur broader interest into MP to facilitate academic and translational development of MP.     

Haloacetaldehyde polymers and macromolecular asymmetry

Polyhaloaldehydes play a special role in aldehyde polymerization. The most prominent trihaloacetaldehyde polymer, polytrichloroacetaldehyde, opened the door to new concepts in polymer chemistry: first, cryotachensic polymerization, the separation of the initiation step from the propagation steps with the ceiling temperature principle for the fabrication of insoluble and infusible polymers, and second, the concept of macromolecular asymmetry and stereospecific and conformationally specific polymerization. Trichloroacetaldhyde could be readily polymerized with a wide range of anionic (and also some cationic) initiators. When the anionic polymerization was initiated with chiral anions, it gave polychloral of one helix sense. To understand the genesis of the polymerization, the oligomerization was investigated to learn how the stereochemistry of the polymerization was established, also in chiral form. All 10 fluoro‐, chloro‐, and bromo‐substituted trihaloacetaldehydes were synthesized as necessary and polymerized, and the polymers were investigated. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2623–2634, 2000